Limits...
Detection and frequency of recombination in tomato-infecting begomoviruses of South and Southeast Asia.

Prasanna HC, Rai M - Virol. J. (2007)

Bottom Line: Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange.Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity.These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia.

View Article: PubMed Central - HTML - PubMed

Affiliation: Indian Institute of Vegetable Research, P B 5002, P 0-B H U, Varanasi, Uttar Pradesh, 221005, India. prasanahc@yahoo.com

ABSTRACT

Background: Tomato-infecting begomoviruses are widely distributed across the world and cause diseases of high economic impact on wide range of agriculturally important crops. Though recombination plays a pivotal role in diversification and evolution of these viruses, it is currently unknown whether there are differences in the number and quality of recombination events amongst different tomato-infecting begomovirus species. To examine this we sought to characterize the recombination events, estimate the frequency of recombination, and map recombination hotspots in tomato-infecting begomoviruses of South and Southeast Asia.

Results: Different methods used for recombination breakpoint analysis provided strong evidence for presence of recombination events in majority of the sequences analyzed. However, there was a clear evidence for absence or low Recombination events in viruses reported from North India. In addition, we provide evidence for non-random distribution of recombination events with the highest frequency of recombination being mapped in the portion of the N-terminal portion of Rep.

Conclusion: The variable recombination observed in these viruses signified that all begomoviruses are not equally prone to recombination. Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange. Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity. These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia.

Show MeSH

Related in: MedlinePlus

TreeOrder Scan of tomato-infecting begomoviruses sequences. Changes in tree order(Y axis) resulting from changes in phylogenetic relationships at 70% bootstrap level are shown for sequential 300 bases sequence fragments at 100 base fragment intervals (X axis). Sequences are assigned to groups based on geographical locations and groups are color coded as indicated by labels. The genome map drawn to scale has been superimposed to indicate the positions of genes in DNA A sequences. Positions were drawn relative to the ToLCGV-[Var] strain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2170441&req=5

Figure 2: TreeOrder Scan of tomato-infecting begomoviruses sequences. Changes in tree order(Y axis) resulting from changes in phylogenetic relationships at 70% bootstrap level are shown for sequential 300 bases sequence fragments at 100 base fragment intervals (X axis). Sequences are assigned to groups based on geographical locations and groups are color coded as indicated by labels. The genome map drawn to scale has been superimposed to indicate the positions of genes in DNA A sequences. Positions were drawn relative to the ToLCGV-[Var] strain.

Mentions: Different methods used for recombination breakpoint analysis also provided strong evidence for presence of past recombination events in most of the sequences analysed. For each of the 32 potential recombinant sequences identified, possible breakpoint positions, sequence fragments and parental genotypes are listed in Table 1. Tomato leaf curl virus from the Philippines and ToLCBV, ToLCBV-[Ban4] and ToLCBV-[Ban5] from Bangalore, south India appeared to be the most complex recombinants carrying evidence of seven and six recombination events respectively. On the opposite end of the spectrum, Tomato leaf curl virus strains including ToLCNDV-Mld and ToLCNDV-[Luc] from New Delhi, ToLCNDV-Svr [Jes] from Bangladesh, and TYLCCNV-Tb [Y38] from China each carried evidence of only a single recombination event. In addition, viruses from geographically well separated regions appeared to have recombined at some time in the past. For example, tomato leaf curl virus strains from Bangalore and Gujarat in India contained sequences closely resembling those found in a ToLCTWV isolate from Taiwan. Also, Chinese viruses contained fragments of sequence closely resembling those found in sequences sampled in Thailand, Taiwan, Bangladesh and South India. Further, we used the TreeOrderScan method [31] to investigate the phylogenetic evidence for recombination in the sequence alignment. This analysis revealed major deviations in the branching order of sequences within trees constructed from different portions of the multiple sequence alignment (Fig. 2). Frequent tree order changes were observed at the region of rep and AC4. Importantly, most of the viruses detected as recombinants in the breakpoint analysis exhibited deviations in their branching order indicating that they were most likely correctly identified as recombinants. In addition, the TreeOrderScan analysis also provided evidence for gene flow amongst viruses in geographically separated regions. For instance, sequences found in southern Indian viruses grouped with those found in Thailand and Bangladesh virus positions from 2335–2652. Thai viruses contained sequences resembling those of Chinese viruses between 300–490 and 590–2372, but Indian viruses between 2472–2743. The recombination observed between geographically separated species/strains probably represents older events as they presumably occurred before their present separation [19]. Movement of vectors and/or infected plant materials may also have contributed to the gene flow observed between these widely separated locations [32]. Alternatively, it is possible that current sampling of Asian begomovirus diversity is so sparse that we do not yet fully appreciate the geographical range of many of the species studied here.


Detection and frequency of recombination in tomato-infecting begomoviruses of South and Southeast Asia.

Prasanna HC, Rai M - Virol. J. (2007)

TreeOrder Scan of tomato-infecting begomoviruses sequences. Changes in tree order(Y axis) resulting from changes in phylogenetic relationships at 70% bootstrap level are shown for sequential 300 bases sequence fragments at 100 base fragment intervals (X axis). Sequences are assigned to groups based on geographical locations and groups are color coded as indicated by labels. The genome map drawn to scale has been superimposed to indicate the positions of genes in DNA A sequences. Positions were drawn relative to the ToLCGV-[Var] strain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2170441&req=5

Figure 2: TreeOrder Scan of tomato-infecting begomoviruses sequences. Changes in tree order(Y axis) resulting from changes in phylogenetic relationships at 70% bootstrap level are shown for sequential 300 bases sequence fragments at 100 base fragment intervals (X axis). Sequences are assigned to groups based on geographical locations and groups are color coded as indicated by labels. The genome map drawn to scale has been superimposed to indicate the positions of genes in DNA A sequences. Positions were drawn relative to the ToLCGV-[Var] strain.
Mentions: Different methods used for recombination breakpoint analysis also provided strong evidence for presence of past recombination events in most of the sequences analysed. For each of the 32 potential recombinant sequences identified, possible breakpoint positions, sequence fragments and parental genotypes are listed in Table 1. Tomato leaf curl virus from the Philippines and ToLCBV, ToLCBV-[Ban4] and ToLCBV-[Ban5] from Bangalore, south India appeared to be the most complex recombinants carrying evidence of seven and six recombination events respectively. On the opposite end of the spectrum, Tomato leaf curl virus strains including ToLCNDV-Mld and ToLCNDV-[Luc] from New Delhi, ToLCNDV-Svr [Jes] from Bangladesh, and TYLCCNV-Tb [Y38] from China each carried evidence of only a single recombination event. In addition, viruses from geographically well separated regions appeared to have recombined at some time in the past. For example, tomato leaf curl virus strains from Bangalore and Gujarat in India contained sequences closely resembling those found in a ToLCTWV isolate from Taiwan. Also, Chinese viruses contained fragments of sequence closely resembling those found in sequences sampled in Thailand, Taiwan, Bangladesh and South India. Further, we used the TreeOrderScan method [31] to investigate the phylogenetic evidence for recombination in the sequence alignment. This analysis revealed major deviations in the branching order of sequences within trees constructed from different portions of the multiple sequence alignment (Fig. 2). Frequent tree order changes were observed at the region of rep and AC4. Importantly, most of the viruses detected as recombinants in the breakpoint analysis exhibited deviations in their branching order indicating that they were most likely correctly identified as recombinants. In addition, the TreeOrderScan analysis also provided evidence for gene flow amongst viruses in geographically separated regions. For instance, sequences found in southern Indian viruses grouped with those found in Thailand and Bangladesh virus positions from 2335–2652. Thai viruses contained sequences resembling those of Chinese viruses between 300–490 and 590–2372, but Indian viruses between 2472–2743. The recombination observed between geographically separated species/strains probably represents older events as they presumably occurred before their present separation [19]. Movement of vectors and/or infected plant materials may also have contributed to the gene flow observed between these widely separated locations [32]. Alternatively, it is possible that current sampling of Asian begomovirus diversity is so sparse that we do not yet fully appreciate the geographical range of many of the species studied here.

Bottom Line: Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange.Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity.These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia.

View Article: PubMed Central - HTML - PubMed

Affiliation: Indian Institute of Vegetable Research, P B 5002, P 0-B H U, Varanasi, Uttar Pradesh, 221005, India. prasanahc@yahoo.com

ABSTRACT

Background: Tomato-infecting begomoviruses are widely distributed across the world and cause diseases of high economic impact on wide range of agriculturally important crops. Though recombination plays a pivotal role in diversification and evolution of these viruses, it is currently unknown whether there are differences in the number and quality of recombination events amongst different tomato-infecting begomovirus species. To examine this we sought to characterize the recombination events, estimate the frequency of recombination, and map recombination hotspots in tomato-infecting begomoviruses of South and Southeast Asia.

Results: Different methods used for recombination breakpoint analysis provided strong evidence for presence of recombination events in majority of the sequences analyzed. However, there was a clear evidence for absence or low Recombination events in viruses reported from North India. In addition, we provide evidence for non-random distribution of recombination events with the highest frequency of recombination being mapped in the portion of the N-terminal portion of Rep.

Conclusion: The variable recombination observed in these viruses signified that all begomoviruses are not equally prone to recombination. Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange. Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity. These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia.

Show MeSH
Related in: MedlinePlus